Ben & Ashley's Molecular Modeling Site

Quantum Calculations Through Computer Exploration

Ashley Hellenbrand & Ben Batura

INTRODUCTION

The electronic structure of a molecule determines much of its reactivity. If given a description of the most probable locations of electrons and their energies, one may be able to predict useful information such as vibrational frequencies, probability of absorption of visible light, molecular dipole moment and polarizability. These electronic structure calculations can now be performed by computers with software packages. These computer programs have the ability to optimize geometry and energy calculations. This experiment optimized the geometry calculations of Br2, SO2 and C8H6. This saves time, money and materials. With the help of computers, large basis sets with the purpose to improve the predictions of energies and geometries are available to calculate some of the largest molecules. That is if there is enough time and memory capability. The modern programs have excellent graphics capabilities which allow us to view three dimensional representations of molecules and/or molecular orbital’s. However, computer programs must be analyzed because they are not always accurate. MOPAC uses empirical data and estimates the values for two electron overlap integrals. The ab initio theories can be used to calculate the optimized geometry, HOMO and LUMO orbitals, dipole moments, and vibrational frequencies of the molecules. The potential energy versus bond length for Br2 showed that the bigger the basis set the better the geometry. A UV-Vis spectrum for the sulfur dioxide was used to compare the calculations for each of the transitional energies of each basis set to sulfur dioxide.

Br₂
The name Bromine originates from the Greek word 'Bromos' meaning "stench." Bromine was discovered by Antoine J. Balard in France in 1826. Bromine is classified as an element in the 'Halogens' section which can be located in group 7 of the Periodic Table. The term "halogen" means "salt-former" and compounds containing halogens are called "salts".
Bromine occurs in nature as bromide salts in Sea Water. Its primary producers are in the USA and Israel. Common uses of bromine include: gasoline antiknock mixtures, fumigants, poisons, dyes, photographic chemicals, medicinal and brominated vegetable oil

Go to the bromine page

SO₂
Sulfur dioxide is a colorless gas with a suffocating, choking odor. It is toxic to humans and concentrations as low as 8 ppm will produce coughing. It is released naturally into the atmosphere from volcanoes and combustion processes. Human impact the environment with sulfur dioxide from the combustion of sulphurous fossil fuels (e.g. coal, oil, natural gas) in power and heating plants, in industry, in household use and the increasing amount of traffic. Inhaling sulfur dioxide is associated with increased respiratory symptoms and disease, difficulty in breathing, and premature death. Sulfur dioxide is sometimes used as a preservative for dried apricots and other dried fruits owing to its antimicrobial properties, used in winemaking, is useful in reducing bleach in papers and delicate materials such as clothes, is a candidate material for refrigerants because of its ease at condensing and possessing a high temperatures of evaporation and is also used as a reagent and solvent in the laboratory.

Go to the sulphur dioxide page

C8H6
Phenylacetylene is an alkyne hydrocarbon containing a phenyl group. It is a colorless liquid or can be ordered clear yellow. In research it is sometimes used as an analog for acetylene because it is easier to handle as a liquid than acetylene gas. Phenylacetylene can cause damage to a person’s blood or upper respiratory tract. Other toxic effects include serious hazards if ingested or inhaled. There may also be s skin irritation if the skin comes in contact with the chemical.

Go to the phenylacetylene page

EXPERIMENTAL

    The molecules Br2, sulfur dioxide (SO2), and phenylacetylene (C8H6) were built on the UWO Quantum Server (WebMO). The MoPAC’s Hamiltonians optimized geometry program was mostly used to get initial geometries of the three molecules. If the calculation failed, the raw output file was searched for the word “failure” to see what occurred. MacMolPlt generated starting points for additional calculations and was used in further examining the results of the calculations. Once the geometries were optimized, the results were transferred to a TextEditor file where they were saved as .log files. The files were made to plain text and saved as “.log” which was then opened in MacMolPlt. The molecules then had their geometry optimized using mechanics and calculations run through three levels ab initio of theory: 321G, 631G and DZV. The lowest level was run first and used as the input file for the next level of theory calculations. For example, 321-G was used for the starting point for 631-G. This made for calculations that had the ability to build off of each other. Each level was saved as a specific .inp file. These files were queued and run using GTK-GAMESS. Once all the levels of theory were complete, they could be used to find the bond lengths, bond angles, and HOMO and LUMO orbitals in MacMolPlt.
    The dipole moments were found by opening the .log files in TextEditor and searching for “electrostatic moment.” For the vibrational frequencies calculations, after molecules obtained their fully optimized calculations with the calculation type set to hessian, the files were saved as another .inp file. This new file was uploaded into TextEditor and the words “vibrational frequency” was searched for each molecule. The potential energy surface verses bond length for Br2 was generated in MacMolPlt and run through GTK-GAMESS. Using the best level of theory for SO2, a UV-Vis transition calculation was run and saved as a .inp file. This was then run through GTK-GAMESS generating a .log file. This file was opened in TextEditor and the words “dipole moments” were searched and recorded.
    The dibromine, sulfur dioxide and phenylacetylene log files were opened with Jmol to create the models of bond lengths, bond angles, and HOMOand LUMO orbitals for this webpage. The Jmol files were saved together and opened in Kompozer to generate the template that would later be set as the webpage.

References:
(1) Mihalick, J.; Gutow, J. Quantum Calculations I. Oshkosh, WI, 2009.
(2) Gutow, J. Molecular Orbitals/ Quantum Calculation Experiment 2. Oshkosh, WI, 2009.

Based on template by A. Herráez as modified by J. Gutow

Page skeleton and JavaScript generated by export to web function using Jmol 11.8.20 2010-02-28 19:28 on Mar 17, 2010.

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